| Variant ID: vg1126361876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26361876 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 84. )
CCTGGGTGCTGGCGGACGGTCCGCCACCACCAAGACCTCCGGCGCCGCCACTACCGGTTCCGCGTCGTCAAGACGGAGGGCGCGGCGAGCGGCGGCTGCT[G/T]
CACGCCATTCGGCTACCACTCCCTCGTCGGCGCCTCCGACTCGGGAGGATCAGCATGAAGAGCCGGATGCCCGCCTCGACATCGAGCGCCGATGTAGTGA
TCACTACATCGGCGCTCGATGTCGAGGCGGGCATCCGGCTCTTCATGCTGATCCTCCCGAGTCGGAGGCGCCGACGAGGGAGTGGTAGCCGAATGGCGTG[C/A]
AGCAGCCGCCGCTCGCCGCGCCCTCCGTCTTGACGACGCGGAACCGGTAGTGGCGGCGCCGGAGGTCTTGGTGGTGGCGGACCGTCCGCCAGCACCCAGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.10% | 0.50% | 22.49% | 61.96% | NA |
| All Indica | 2759 | 6.40% | 0.00% | 17.04% | 76.59% | NA |
| All Japonica | 1512 | 28.80% | 1.50% | 30.09% | 39.68% | NA |
| Aus | 269 | 20.40% | 0.00% | 40.15% | 39.41% | NA |
| Indica I | 595 | 2.70% | 0.00% | 10.08% | 87.23% | NA |
| Indica II | 465 | 4.30% | 0.00% | 11.83% | 83.87% | NA |
| Indica III | 913 | 7.80% | 0.00% | 23.33% | 68.89% | NA |
| Indica Intermediate | 786 | 8.80% | 0.00% | 18.07% | 73.16% | NA |
| Temperate Japonica | 767 | 40.50% | 0.80% | 8.47% | 50.20% | NA |
| Tropical Japonica | 504 | 9.10% | 2.20% | 63.29% | 25.40% | NA |
| Japonica Intermediate | 241 | 32.40% | 2.10% | 29.46% | 36.10% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 13.54% | 54.17% | NA |
| Intermediate | 90 | 16.70% | 1.10% | 18.89% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126361876 | G -> T | LOC_Os11g43670.1 | missense_variant ; p.Ala153Ser; MODERATE | nonsynonymous_codon ; A153S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | nan | DELETERIOUS | 0.01 |
| vg1126361876 | G -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |